Surveying expression level polymorphism and single-feature polymorphism in near-isogenic wheat lines differing for the Yr5 stripe rust resistance locus

  • Tristan E. Coram
  • Matthew L. Settles
  • Meinan Wang
  • Xianming Chen
Original Paper


DNA polymorphisms are valuable for several applications including genotyping, molecular mapping and marker-assisted selection. The 55 K Affymetrix Wheat GeneChip was used to survey expression level polymorphisms (ELPs) and single-feature polymorphisms (SFPs) between two near-isogenic wheat genotypes (BC7:F4) that differ for the Yr5 stripe rust resistance locus, with the objective of developing genetic markers linked to Yr5. Ninety-one probe sets showing ELPs and 118 SFP-containing probe sets were identified between isolines, of which just nine ELP probe sets also contained SFPs. The proportion of the transcriptome estimated to be variable between isolines from this analysis was 0.30% for the ELPs and 0.39% for the SFPs, which was highly similar to the theoretical genome difference between isolines of ~0.39%. Using wheat-rice synteny, both ELPs and SFPs mainly clustered on long arms of rice chromosomes four and seven, which are syntenous to wheat chromosomes 2L (Yr5 locus) and 2S, respectively. The strong physical correlation between the two types of polymorphism indicated that the ELPs may be regulated by cis-acting DNA polymorphisms. Twenty SFPs homologous to rice 4L were used to develop additional genetic markers for Yr5. Physical mapping of the probe sets containing SFPs to wheat chromosomes identified nine on the target chromosome 2BL, thus wheat-rice synteny greatly enhanced the selection of SFPs that were located on the desired wheat chromosome. Of these nine, four were converted into polymorphic cleaved amplified polymorphic sequence (CAPS) markers between Yr5 and yr5 isolines, and one was mapped within 5.3 cM of the Yr5 locus. This study represents the first array-based polymorphism survey in near-isogenic genotypes, and the results are applied to an agriculturally important trait.

Supplementary material

122_2008_784_MOESM1_ESM.doc (1.8 mb)
Normalized expression and residual plots for the 9 expression level polymorphism (ELP) probe sets that also contained single-feature polymorphisms (SFPs) detected between the Yr5 and yr5 wheat isolines. The ‘normalized data’ plot shows robust robust multi-array average (RMA) background corrected and quantile-normalized expression log intensity values (y-axis) for each probe (x-axis) in the probe set. Horizontal lines indicate the expression summary value calculated for the probe set and vertical lines indicate the position of called SFPs. The ‘residual data’ plot shows the residuals after removing the expression effect that was used to detect SFPs. Vertical lines indicate positions of called SFPs. In both plots the black lines represent Yr5 GeneChip data and red lines represent yr5 data. Each figure is labeled with the probe set ID and also the result after visual inspection. (DOC 1879 kb)
122_2008_784_MOESM2_ESM.doc (189 kb)
Expression level polymorphisms (ELPs) detected between the Yr5 and yr5 wheat isolines, where ‘Isoline’ indicates the isoline with the significantly higher expression, and ‘Condition’ refers to Puccinia striiformis f. sp. tritici-inoculation (Pst), mock-inoculation (Mock) or both treatments (Both). ‘Rice chromosome’ indicates the rice chromosome to which each probe set had the highest sequence homology, if significant. Functional categories were based on the Munich Information Center for Protein Sequences classifications and putative function shows the best significant BLASTX database hit from HarvEST. NA indicates no significant homology. (DOC 189 kb)
122_2008_784_MOESM3_ESM.doc (582 kb)
Significant single-feature polymorphisms (SFPs) detected between the Yr5 and yr5 wheat isolines after applying significance analysis of microarrays (SAM). The sign of the d value indicates which isoline was polymorphic with regard to the reference GeneChip oligo (positive values predicted SFPs in Yr5 and negative values in yr5). ‘stdev’ refers to standard deviation of the d value, ‘rawp’ is the P value, ‘q.value’ is the adjusted P value after multiple testing correction, and ‘R.fold’ is the fold change between isolines using yr5 data as the reference. (DOC 582 kb)
122_2008_784_MOESM4_ESM.doc (160 kb)
Single-feature polymorphisms (SFPs) detected between the Yr5 and yr5 wheat isolines, where ‘Probes’ refers to the number of SFP probes within the probe set. ‘Rice chromosome’ indicates the rice chromosome to which each probe set had the highest sequence homology, if significant. Functional categories were based on the Munich Information Center for Protein Sequences classifications and putative function shows the best significant non-redundant BLASTX database hit from HarvEST. Probe sets marked with an asterisk were also identified as expression level polymorphisms (ELPs). NA indicates no significant homology. (DOC 159 kb)


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Copyright information

© Springer-Verlag 2008

Authors and Affiliations

  • Tristan E. Coram
    • 1
    • 2
  • Matthew L. Settles
    • 3
  • Meinan Wang
    • 2
  • Xianming Chen
    • 1
    • 2
  1. 1.US Department of AgricultureAgricultural Research Service, Wheat Genetics, Quality, Physiology and Disease Research UnitPullmanUSA
  2. 2.Department of Plant PathologyWashington State UniversityPullmanUSA
  3. 3.Department of Molecular BiosciencesWashington State UniversityPullmanUSA

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